Amino acids

R-groups non-polarpolaracidicbasic

proteins condensation between carboxylic acids and amines

+ + H2O

carboxylic acid amine amide

CO

OHNH C

O

N

Amides

amides resonance structure

alanine glycine Ala-Gly +H2O

dipeptide

CO

NC

O

N

CH2N

H

CO

OHCH3

CH2N

H

CO

OHH

CH2N

H

CO

H

CN

H

CO

OHHCH3

Polypeptides“backbone”

N1-C1-C1-N2-C2-C2-N3-C3-C3-

peptide bonds

_

H_H =

OOH

_

H_

H

=O

=

O

_R _R _

R

N-terminal residue

C-terminalresidue

biological activity = structure

protein structure 4 levels

Primary structure

sequence of amino acids

hemoglobin transports O2 and CO2 4 protein chains 300 amino acids

6th amino acid from N-terminus

Glu Val

-CH2CH2-CO2H -CH(CH3)2

R

Sickle cell anemia

water soluble water insoluble

Secondary structure

hydrogen bonding backbone groups

H-bond donors

N1-C1-C1-N2-C2-C2-N3-C3-C3-

_

H_H =

OOH

_

H

_

H

=

O

=

O

_R _R _

R

H-bond acceptors

Two main secondary structures: -helix

-sheet

Alpha helix

Every C=O bonded to N-H 4 residues away

forms a helix core is backbone

R-groups outside

3.6 amino acids per turn

proline

breaks helix

=

O

C

no H-bondingC=

O

N

H

Beta sheet

Every C=O bonded to N-H far apart in 1o structureon different chains

peptide chains extended side-by-side

maximal H-bonding for anti-parallel chains

small R-groups above and below the sheet

if not -helix or -sheet random coil

Proteins

1o structure amino acid sequence

2o structure - helix -sheet

H-bonding betweenC=O and N-H of backbone

- +

some proteins only have 1o and 2o structure:

fibroin (silk) -sheet

keratincollagen

hairskin

- helixinsoluble in H2O

non-polar residues

Fibrous

Disulfide bonds

cysteine -CH2-SH

S-H H-S C

H

N

C

C

H

N

C

reduced

[O]

S S C

H

N

C

C

H

N

C

oxidized

Gly-Glu- His-Ala-Phe-Ser-Ser-Val- His-Ile-Met-Arg-Asp-Val- Asn-

Tertiary structurePrimary structure sequence of amino acids

Alanine

Non-polar

Phenylalanine

Polar

Serine

Valine

Acidic or Basic

Glutamic acidHistidine

Isoleusine Methionine

Arginine

AsperagineAspartic acid

Glycine

Ala-Phe-Ser-Ser-Val-Glu-His-Ile-Met-Arg-Asp-Val-His-Asn-Gly

Tertiary structureAla-Phe-Ser-Ser-Val-Glu-His-Ile-Met-Arg-Asp-Val-His-Asn-Gly

arrange these in an -helix

Ala 1

Phe2

Ser3

Ser

4

Val 5Glu

6

His7

Ile8

Met9

Arg10

Asp11

Val 12

His13

Asn14

Gly15

non-polarpolarinterior

exterior

Tertiary structure

interaction of the R-groups-

-

+

-+

-

- +

proteins fold aroundnon-polar groups

globular proteins

hydrophobic residues inside

polar and charged residues outside

Tertiary structure

1. Hydrophobic interactions non-polar R-groups

LDF2. Hydrogen bonding

between H-bonddonors and acceptors

polar R-groups

3. Ionic bonds (salt bridges) acidic and basic R-groups

4. Covalent bonds (disulfide) cysteins

ion-ion

interactions of R-groups

CH3

NH+

N-terminus

C-terminus

Pro

Ala Phe

Arg

Asp

Pro

SS Cys

Cys

His

His

-O-CH O

= Fe2+

Denaturing treatments

1. Heat above 50-60oC frying eggsunburn

2. pH disrupt salt bridgesapproach pHI

3. detergents unfold globular proteins SDS

SO4-

Na+

-

-

+

-+

-

- +

Denaturing treatments4. reducing agents

S-S SH HS

5. Metal salts Hg+, Pb+, Ag+ S-Hg

C =O_O-

Hg+

6. H-bonding solvents alcoholacetone

7. “Chaotropes”

urea guanidine

oxidizing agents

CH2N NH2

O

CH2N NH2

NH